It's a UI issue and not really an issue with how Fediverse communities work, if the same link is posted in multiple communities it should ideally show you only one of them in your feed. The user would be able to specify how he wants to discriminate between the same links: most recent one, most active one etc... It shouldn't be difficult to do at the UI level.
That could be a user setting, just like you specify how you want to rank the threads in your feed, you could specify also how to discriminate between threads that are sharing the same link: you could say you want the most recent one for example. Again, this could easily be done at the UI level.
This sounds good in theory, but it's going to be difficult if the communities have different rules. A comment made on the post in Community 1 might be okay IN Community 1 but innappropiate in Community 2 ... how would you deal with this if the comment section was merged and appeared in both communties?
And that is IMO a false problem. It is perfectly okay to have completely different discussions around the same link, just like currently you can have the same link shared on Reddit, Hacker News and other link aggregators and you obviously end up with completely different discussions around the same link.
This whole "there's too much fragmentation" drama is IMO a false problem raised by people who don't fully understand that the Fediverse does not mean that you will have one single big entity with synchronized rules and one single community per topic globally. It means that you will have something like multiple independently run "forums", with different vibes and potentially different moderation rules, and users in federated "forums" can easily hop from one to another with the same account. It doesn't mean that you'll have one single large Reddit replacement with communities that are deemed "similar" forcibly merged to prevent the false problem of "fragmentation".
The internet would be in a completely sorry state if only one forum per topic was allowed.
It is perfectly okay to have completely different discussions around the same link
thats not whats happening. you're either getting the same comments in all places or you're arbitrarily preventing people from commenting all in 1 place to prop up this guise of "freedom" that exists at the will of the instance admins.